3D Motifs Research Articles

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.

Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring structure-based sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.

Use of resistivity and density borehole image logs to identify and distribute facies in the Pikka unit — A case study from the Nanushuk Formation, North Slope, Alaska

Over the past few decades, the North Slope of Alaska has yielded several major hydrocarbon discoveries in the deltaic topsets of the Brookian Nanushuk Formation. Together, the Nanushuk topsets and genetically related foreset and bottomset beds of the Torok Formation comprise part of a giant clinothem system that prograded across the Colville Foreland Basin during the lower Cretaceous (the Aptian through the Cenomanian). The Nanushuk Topset Play contains stratigraphically trapped hydrocarbons within multiple fairways trending roughly north to south along the basin’s extent. Inside the Pikka Unit, the Nanushuk Formation represents a shelf-edge delta and attached shoreface system, defined primarily from sedimentological interpretations of conventional cores integrated with 3D seismic reflection data and well-log motifs. In this study, we build a structural and stratigraphic framework for the Nanushuk reservoir across the Pikka Unit through integrated observations of the borehole image logs, seismic data, and core. In the described workflow, the boundaries delimiting dip zones interpreted in the wells are correlated to higher order stratigraphic cycles within the Nanushuk clinothem zone. These boundaries are observed in seismic profiles and provide the basis of the structural framework. In addition, core facies interpretations are calibrated to CT-scan data to establish each facies character and vertical distribution within the wells. In the absence of core data, core-calibrated borehole images are instrumental in guiding sedimentological and structural interpretations. This extrapolation is dependent on the image log quality and resolution. The calibrated facies interpretations are applied to wells without core data and guided by seismic amplitude interpretation to extrapolate reservoir presence and distribution across the area.

Vacuum-solvent thermal synthesis of nickel foam-supported CuO-based sensor electrode for good electrochemical detection of nitrite

Given the bad effect of superfluous nitrites on biology/environment, engineering the fast, sensitive, and real-time quantification of nitrites matters to safeguard both the eco-system and human public health. Here, a CuO nanocatalyst self-supported on nickel foam (CuO@NF) was crafted via facilely fusing a vacuum solvent recipe with ambient thermal annealing. Various characterizations show that hollow sea urchin-like CuO structures were arrayed on substrate to feature a 3D porous motif and large specific surface area. Such traits promise the effective local wetting and enrichment of nitrite to augment the nitrate capture/contact capacity, underlying a highly sensitive electrochemical determination of nitrite. Specifically, a wide linear detection range can span 0.5 to 4250 μM, with a stable current response at a concentration as low as 0.5 μM nitrite. The detection limit or sensitivity is approximately 0.0287 mM or 2.402 mAmM−1 cm−2, respectively. This electrode was also successfully applied to detect the nitrite in complex samples like pickled vegetables with satisfactory recovery rates. Our study shows that the self-supported CuO sensor provides an ingenious tactic to build high-efficiency binderless electrodes for the electrochemical sensing applications.

PERFUMES: pipeline to extract RNA functional motifs and exposed structures.

Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs relies on their ability to fold into 3D structures. Specifically, nucleotides inside secondary structure loops form non-canonical base pairs that help stabilize complex local 3D structures. These RNA 3D motifs can promote specific interactions with other molecules or serve as catalytic sites. We introduce PERFUMES, a computational pipeline to identify 3D motifs that can be associated with observable features. Given a set of RNA sequences with associated binary experimental measurements, PERFUMES searches for RNA 3D motifs using BayesPairing2 and extracts those that are over-represented in the set of positive sequences. It also conducts a thermodynamics analysis of the structural context that can support the interpretation of the predictions. We illustrate PERFUMES' usage on the SNRPA protein binding site, for which the tool retrieved both previously known binder motifs and new ones. PERFUMES is an open-source Python package (https://jwgitlab.cs.mcgill.ca/arnaud_chol/perfumes).

Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases.

Plant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the specificity or functional-related features of PdiTPSs are not well understood. For a more profound insight, we collected, constructed, and curated 199 functionally characterized PdiTPSs and their corresponding 3D structures. The complex correlations among their sequences, domains, structures, and corresponding products were comprehensively analyzed. Ultimately, our focus narrowed to the geometric arrangement of local structures. We found that local structural alignment can rapidly localize product-specific residues that have been validated by mutagenesis experiments. Based on the 3D motifs derived from the residues around the substrate, we successfully searched diterpene synthases (diTPSs) from the predicted terpene synthases and newly characterized PdiTPSs, suggesting that the identified 3D motifs can serve as distinctive signatures in diTPSs (I and II class). Local structural analysis revealed the PdiTPSs with more conserved amino acid residues show features unique to class I and class II, whereas those with fewer conserved amino acid residues typically exhibit product diversity and specificity. These results provide an attractive method for discovering novel or functionally equivalent enzymes and probing the product specificity in cases where enzyme characterization is limited.

Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.

The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of noncanonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops. We previously developed the integer programming framework RNA Motifs over Integer Programming (RNAMoIP) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all nonredundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information, and (iv) noncanonical motifs at kink-turn locations. The source code of the framework is available at https://gitlab.info.uqam.ca/cbe/RNAMoIP and an interactive web server at https://rnamoip.cbe.uqam.ca/.

NRAMP gene family in Kandelia obovata: genome-wide identification, expression analysis, and response to five different copper stress conditions.

Natural resistance-associated macrophage proteins (NRAMPs) are a class of metal transporters found in plants that exhibit diverse functions across different species. Transporter proteins facilitate the absorption, distribution, and sequestration of metallic elements within various plant tissues. Despite the extensive identification of NRAMP family genes in various species, a full analysis of these genes in tree species is still necessary. Genome-wide identification and bioinformatics analysis were performed to understand the roles of NRAMP genes in copper (CuCl2) stress in Kandelia obovata (Ko). In Arachis hypogaea L., Populus trichocarpa, Vitis vinifera, Phaseolus vulgaris L., Camellia sinensis, Spirodela polyrhiza, Glycine max L. and Solanum lycopersicum, a genome-wide study of the NRAMP gene family was performed earlier. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and CuCl2 were all investigated in this research. In order to comprehend the notable functions of the NRAMP gene family in Kandelia obovata, a comprehensive investigation was conducted at the genomic level. This study successfully found five NRAMP genes, encompassing one gene pair resulting from whole-genome duplication and a gene that had undergone segmental duplication. The examination of chromosomal position revealed an unequal distribution of the KoNRAMP genes across chromosomes 1, 2, 5, 7, and 18. The KoNRAMPs can be classified into three subgroups (I, II, and SLC) based on phylogeny and synteny analyses, similar to Solanum lycopersicum. Examining cis-regulatory elements in the promoters revealed five hormone-correlated responsive elements and four stress-related responsive elements. The genomic architecture and properties of 10 highly conserved motifs are similar among members of the NRAMP gene family. The conducted investigations demonstrated that the expression levels of all five genes exhibited alterations in response to different levels of CuCl2 stress. The results of this study offer crucial insights into the roles of KoNRAMPs in the response of Kandelia obovata to CuCl2 stress.

Genome-Wide Identification and Expression Analysis of the Copper Transporter (COPT/Ctr) Gene Family in Kandelia obovata, a Typical Mangrove Plant.

The copper transporter (COPT/Ctr) gene family plays a critical part in maintaining the balance of the metal, and many diverse species depend on COPT to move copper (Cu) across the cell membrane. In Arabidopsis thaliana, Oryza sativa, Medicago sativa, Zea mays, Populus trichocarpa, Vitis vinifera, and Solanum lycopersicum, a genome-wide study of the COPT protein family was performed. To understand the major roles of the COPT gene family in Kandelia obovata (Ko), a genome-wide study identified four COPT genes in the Kandelia obovata genome for the first time. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and Cu were all investigated in this research. Structural and sequence investigations show that most KoCOPTs have three transmembrane domains (TMDs). According to phylogenetic research, these KoCOPTs might be divided into two subgroups, just like Populus trichocarpa. KoCOPT gene segmental duplications and positive selection pressure were discovered by universal analysis. According to gene structure and motif analysis, most KoCOPT genes showed consistent exon-intron and motif organization within the same group. In addition, we found five hormones and four stress- and seven light-responsive cis-elements in the KoCOPTs promoters. The expression studies revealed that all four genes changed their expression levels in response to copper (CuCl2) treatments. In summary, our study offers a thorough overview of the Kandelia obovata COPT gene family's expression pattern and functional diversity, making it easier to characterize each KoCOPT gene's function in the future.

Blue-Emitting 2D- and 3D-Zinc Coordination Polymers Based on Schiff-Base Amino Acid Ligands

The solvothermal reaction of Zn(NO3)2·4H2O, 1-OH-2-naphthaldehyde, and 2-methylalanine (mAla) in MeOH leads to the formation of complex {[ZnL1]}2n (1) (H2L1 = the Schiff-base resulting from the reaction of 1-OH-2-naphthaldehyde and mAla) in good yields. The structure of the neutral species, as determined by single-crystal crystallography, describes a two-dimensional coordination polymer, with repeating {Zn2} units bridged by syn, anti-carboxylate groups of the Schiff-base ligands. Repeating the same reaction using glycine (gly) instead of mAla leads to the formation of complex {[ZnL2]·0.33MeOH}3n (2.0.33MeOH) (H2L2 = the Schiff-base resulting from the reaction of 1-OH-2-naphthaldehyde and gly), again in good yields. Complex 2 describes a three-dimensional coordination polymer based on {Zn2} building blocks, arranged by anti, anti-carboxylate groups in a 3D motif. Complexes 1 and 2 were found to strongly emit at ~435 nm (λexc = 317 nm) both in solution and solid state, with complex 2 displaying a slightly longer lifetime of τav = 2.45 ns vs. τav = 2.02 ns for 1.

More than just pattern recognition: Prediction of uncommon protein structure features by AI methods

The CASP14 experiment demonstrated the extraordinary structure modeling capabilities of artificial intelligence (AI) methods. That result has ignited a fierce debate about what these methods are actually doing. One of the criticisms has been that the AI does not have any sense of the underlying physics but is merely performing pattern recognition. Here, we address that issue by analyzing the extent to which the methods identify rare structural motifs. The rationale underlying the approach is that a pattern recognition machine tends to choose the more frequently occurring motifs, whereas some sense of subtle energetic factors is required to choose infrequently occurring ones. To reduce the possibility of bias from related experimental structures and to minimize the effect of experimental errors, we examined only CASP14 target protein crystal structures determined to a resolution limit better than 2 Å, which lacked significant amino acid sequence homology to proteins of known structure. In those experimental structures and in the corresponding models, we track cis peptides, π-helices, 310-helices, and other small 3D motifs that occur in the PDB database at a frequency of lower than 1% of total amino acid residues. The best-performing AI method, AlphaFold2, captured these uncommon structural elements exquisitely well. All discrepancies appeared to be a consequence of crystal environment effects. We propose that the neural network learned a protein structure potential of mean force, enabling it to correctly identify situations where unusual structural features represent the lowest local free energy because of subtle influences from the atomic environment.

Rotational multimaterial printing of filaments with subvoxel control.

Helical structures are ubiquitous in nature and impart unique mechanical properties and multifunctionality1. So far, synthetic architectures that mimic these natural systems have been fabricated by winding, twisting and braiding of individual filaments1-7, microfluidics8,9, self-shaping1,10-13 and printing methods14-17. However, those fabrication methods are unable to simultaneously create and pattern multimaterial, helically architected filaments with subvoxel control in arbitrary two-dimensional (2D) and three-dimensional (3D) motifs from a broad range of materials. Towards this goal, both multimaterial18-23 and rotational24 3D printing of architected filaments have recently been reported; however, the integration of these two capabilities has yet to be realized. Here we report a rotational multimaterial 3D printing (RM-3DP) platform that enables subvoxel control over the local orientation of azimuthally heterogeneous architected filaments. By continuously rotating a multimaterial nozzle with a controlled ratio of angular-to-translational velocity, we have created helical filaments with programmable helix angle, layer thickness and interfacial area between several materials within a given cylindrical voxel. Using this integrated method, we have fabricated functional artificial muscles composed of helical dielectric elastomer actuators with high fidelity and individually addressable conductive helical channels embedded within a dielectric elastomer matrix. We have also fabricated hierarchical lattices comprising architected helical struts containing stiff springs within a compliant matrix. Our additive-manufacturing platform opens new avenues to generating multifunctional architected matter in bioinspired motifs.

PyScoMotif: discovery of similar 3D structural motifs across proteins.

The fast and accurate detection of similar geometrical arrangements of protein residues, known as 3D structural motifs, is highly relevant for many applications such as binding region and catalytic site detection, drug discovery and structure conservation analyses. With the recent publication of new protein structure prediction methods, the number of available protein structures is exploding, which makes efficient and easy-to-use tools for identifying 3D structural motifs essential. We present an open-source Python package that enables the search for both exact and mutated motifs with position-specific residue substitutions. The tool is efficient, flexible, accurate, and suitable to run both on computer clusters and personal laptops. Two successful applications of pyScoMotif for catalytic site identification are showcased. The pyScoMotif package can be installed from the PyPI repository and is also available at https://github.com/3BioCompBio/pyScoMotif. It is free to use for non-commercial purposes.

Granular Ionogel Particle Inks for 3D Printed Tough and Stretchable Ionotronics.

Ionogels have garnered great attention as promising soft conducting materials for the fabrication of flexible energy storage devices, soft actuators, and ionotronics. However, the leakage of the ionic liquids, weak mechanical strength, and poor manufacturability have greatly limited their reliability and applications. Here, we propose a new ionogel synthesis strategy by utilizing granular zwitterionic microparticles to stabilize ionic liquids. The ionic liquids swell the microparticles and physically crosslink microparticles via either electronic interaction or hydrogen bonding. Further introducing a photocurable acrylic monomer enables the fabrication of double-network (DN) ionogels with high stretchability (>600%) and ultrahigh toughness (fracture energy > 10 kJ/m2). The synthesized ionogels exhibit a wide working temperature of -60 to 90 °C. By tuning the crosslinking density of microparticles and physical crosslinking strength of ionogels, we synthesize DN ionogel inks and print them into three-dimensional (3D) motifs. Several ionogel-based ionotronics are 3D printed as demonstrations, including strain gauges, humidity sensors, and ionic skins made of capacitive touch sensor arrays. Via covalently linking ionogels with silicone elastomers, we integrate the ionogel sensors onto pneumatic soft actuators and demonstrate their capacities in sensing large deformation. As our last demonstration, multimaterial direct ink writing is harnessed to fabricate highly stretchable and durable alternating-current electroluminescent devices with arbitrary structures. Our printable granular ionogel ink represents a versatile platform for the future manufacturing of ionotronics.

Non-canonical base pairing

Non-canonical base pairs are planar hydrogen-bonded pairs of nucleobases, having hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base pairs, as in the classic double-helical DNA. The structures of polynucleotide strands of both DNA and RNA molecules can be understood in terms of sugar-phosphate backbones consisting of phosphodiester-linked D 2’ deoxyribofuranose (D ribofuranose in RNA) sugar moieties, with purine or pyrimidine nucleobases covalently linked to them. Here, the N9 atoms of the purines, guanine and adenine, and the N1 atoms of the pyrimidines, cytosine and thymine (uracil in RNA), respectively, form glycosidic linkages with the C1’ atom of the sugars. These nucleobases can be schematically represented as triangles with one of their vertices linked to the sugar, and the three sides accounting for three edges through which they can form hydrogen bonds with other moieties, including with other nucleobases. As also explained in greater detail later in this article, the side opposite to the sugar-linked vertex is traditionally called the Watson-Crick edge, since they are involved in forming the Watson-Crick base pairs which constitute building blocks of double-helical DNA. The two sides adjacent to the sugar-linked vertex are referred to, respectively, as the Sugar and Hoogsteen (C-H for pyrimidines) edges. Each of the four different nucleobases is characterized by distinct edge-specific distribution patterns of their respective hydrogen bond donor and acceptor atoms, complementarity with which, in turn, define the hydrogen bonding patterns involved in base pairing. The double helical structures of DNA or RNA are generally known to have base pairs between complementary bases, Adenine: Thymine (Adenine: Uracil in RNA) or Guanine: Cytosine. They involve specific hydrogen bonding patterns corresponding to their respective Watson-Crick edges and are considered Canonical Base Pairs. At the same time, the helically twisted backbones in the double helical duplex DNA form two grooves, major and minor, through which the hydrogen bond donor and acceptor atoms corresponding respectively to the Hoogsteen and sugar edges are accessible for additional potential molecular recognition events. Experimental evidence reveals that the nucleotide bases are also capable of forming a wide variety of pairing between bases in various geometries, having hydrogen bonding patterns different from those observed in Canonical Base Pairs [Figure 1]. These base pairs, which are generally referred to as Non-Canonical Base Pairs, are held together by multiple hydrogen bonds and are mostly planar and stable. Most of these play very important roles in shaping the structure and function of different functional RNA molecules. In addition to their occurrences in several double-stranded stem regions, most of the loops and bulges that appear in single-stranded RNA secondary structures form recurrent 3D motifs, where non-canonical base pairs play a central role. Non-canonical base pairs also play crucial roles in mediating the tertiary contacts in RNA 3D structures.

Synthesis and Characterization of a Dysprosium(III)–Iron(III) Heterodinuclear Complex: Crystallographic, Hirshfeld Surface, Density-Functional Theory, and Luminescence Analyses

Here, a new cyano-bridged 3d–4f compound, a Dy(III)–Fe(III) molecular assembly ([Dy(DMF)4(H2O)3(μ-CN)Fe(CN)5.H2O] (1)), having a structure consisting of neutral one-dimensional (1D) chains, as well as an unbound aqua molecule, was synthesized and characterized using single crystal X-ray diffraction (XRD), infrared (IR), and elemental analyses. We then examined its structural topologies and studied its density functional theory (DFT), Hirshfeld surface analyses, and photophysical properties. The 1D chains were further linked by H-bond interactions, generating a three-dimensional (3D) motif which stabilizes the whole molecule. The weak interactions in 1 were assessed using Hirshfeld surface analyses, as well as fingerprint plots and DFT studies. Additionally, Hirshfeld surface analysis was performed to elucidate the roles of the weak interactions, such as the H⋯H, C⋯H, C–H⋯π, and van der Waals (vdW) interactions which are pivotal to stabilizing the crystal environment. Furthermore, the DFT studies were used to elucidate the bonding structure within the complex system. Complex 1 exhibits characteristic fluorescence as the Dy(III) complex is an excellent lime green luminescent material. Thus, it is considered to be a suitable material for preparing photoluminescent material.

Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.).

Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.

ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.

Atomistic models of nucleic acids (NA) fragments can be used to model the 3D structures of specific protein-NA interactions and address the problem of great NA flexibility, especially in their single-stranded regions. One way to obtain relevant NA fragments is to extract them from existing 3D structures corresponding to the targeted context (e.g. specific 2D structures, protein families, sequences) and to learn from them. Several databases exist for specific NA 3D motifs, especially in RNA, but none can handle the variety of possible contexts. This article presents protNAff (protein-bound Nucleic Acids filters and fragments), a new pipeline for the conception of searchable databases on the 2D and 3D structures of protein-bound NA, the selection of context-specific (regions of) NA structures by combinations of filters, and the creation of context-specific NA fragment libraries. The strength of this pipeline is its modularity, allowing users to adapt it to many specific modeling problems. As examples, the pipeline is applied to the quantitative analysis of (i) the sequence-specificity of trinucleotide conformations, (ii) the conformational diversity of RNA at several levels of resolution, (iii) the effect of protein binding on RNA local conformations and (iv) the protein-binding propensity of RNA hairpin loops of various lengths. The source code is freely available for download at URL https://github.com/isaureCdB/protNAff. The database and the trinucleotide fragment library are downloadable at URL https://zenodo.org/record/6483823#.YmbVhFxByV4. Supplementary data are available at Bioinformatics online.

Capturing the geometry, function, and evolution of enzymes with 3D templates.

Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs, or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well as some exemplar cases for examining evolutionary links in enzymes. We also introduce the concept of using more than one template per structure to represent flexible sites, as an approach to better understand catalysis through snapshots captured in enzyme structures. Functional annotation from structure is an important topic that has recently resurfaced due to the new more accurate methods of protein structure prediction. Therefore, we anticipate that template‐based functional site detection will be a powerful tool in the task of characterizing a vast number of new protein models.

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA.

The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.